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BioSQL is a generic unifying relational schema for storing sequences and sequence annotations from different sources, for instance Genbank or Swissprot. It is also well suited to work with phyloninformatics and phylogenetic trees.

BioSQL is meant to be a common data storage layer supported by all the different Bio* projects, Bioperl, Biojava, Biopython, and Bioruby. Entries stored through an application written in, say, Bioperl could be retrieved by another written in Biojava.

There are currently three different RDBMSs supported: MySQL, PostgreSQL, and Oracle.